GeneMapperToFamilias Developed by Antonio Vozmediano and Lourdes Prieto

DNA Laboratory, Comisaria General de Policia Cientifica

(Spanish Forensic Police)

This software, freely available here, was created to facilitate transferring data from GeneMapper

program to Familias (1.97 or 3) program more quickly and safely. A Spanish version of this

document is also available. Input files for the example showed in this document as well as

additional files (kits configuration) are available here.

Improvements from previous versions are:

- Fits any commercial PCR kit.

- Genetic data (nuclear DNA profiles) that can be imported from Genemapper

have increased from 8 to 9 profiles.

- Available in two languages: English or Spanish.

- The txt file generated by GeneMapper can be used directly.

- The name of genetic markers, alleles and their frequencies are imported as

in previous versions (Excel file xls/x). In previous versions an Excel file for

each PCR kit was necessary. In this version you can keep your population

data in only one Excel file, using one sheet for each kit (5 sheets t

maximum).

The steps to follow are:

1. Select the txt file containing the configuration of the PCR kit you have

used to analyze the samples.

2. Create an Excel (xls / x) file containing the allele frequencies of your

population (name of genetic markers, alleles and their frequencies).

3. Generate a txt file from GeneMapper.

4. Open the executable and follow the instructions.

1. Select the “Kit configuration” file (txt)

“Kit configuration” files are available for the following PCR kits: Cofiler, PowerPlex Fusion,

Globalfiler, Identifiler, Minifiler, NGM, NGM-Select, PowerPlex-16, PowerPlex-21, Profiler,

ProfilerPlus, SEfiler, SGM-Plus and Verifiler. You can download them here (zipped “kit

config” folder)

If you are using a different kit you can also create the “kit configuration” txt file as follows:

- Open a new txt file. To move from one line to next one return key should be

used.

- Write the name of the kit in the first line.

- Add the number of genetic markers that your kit contains in the second line.

- Add the number of genetic markers that are not involved in the calculation

in the third line (amelogenin, Y chromosome, etc.).

- Add the position of Amelogenin in the kit in the fourth line.

- Add the position/s where the rest of genetic markers that are not related to

calculation are located in the kit (one number per line)

- Save the file as “kitname_config.txt” (e.g., globalfiler_config.txt)

See the picture as an example for Globalfiler: 24 markers, 3 markers not involved in the

calculations (Y-indel, Amel and DYS391), amel located at position 7th, other markers located in

positions 6th and 11

th.

2. Create an Excel (xls/x) containing the population database

This works as in previous versions but it has been improved. The order of markers in the

population database has to be the same as the ones generated in the GeneMapper txt.

GeneMappertoFamilias does not check the name of the markers, but only the order of markers

involved in the calculation.

In previous versions of GeneMappertoFamilias you needed an Excel population file per PCR

kit. Now you can create a single Excel file containing population data for several PCR kits by

adding each data for each PCR kit in one sheet of the file (5 worksheets at maximum).

See the picture as an example (note that Yindel, amelogenin and DYS391 are excluded):

3. Generate a txt file from GeneMapper

1. Open the Project of interest in GeneMapper

2. Go to the “Genotypes” tab

3. In the upper menu, go to “Table settings” and select “Traditional Allele Table”

4. In the upper menu select the “Export Table” button

5. Export the table in txt format and save it where you desire. This table contains the data

of all the samples that were analysed in the project (including Ladders, negative

controls, etc.)

4. Open the executable “GeneMappertoFamilias” and follow the steps.

The first screen of the executable allows you to select the language (English or Spanish).

Value 1 is Spanish.

Any other value or action is English.

Take into account that this option cannot be changed after this step.

Click OK.

A screen with three tabs ('Home', 'Import' and 'To Familias 1.97 or 3') will be opened:

4.1. HOME TAB

This tab contains 4 sections: kit configuration, Options, Individuals and Sheet

4.1.1. Kit configuration section (load txt file): Import the kit configuration txt file of

interest (e.g. Globalfiler_config). You cannot change this file during the following

steps (if you want to change the kit you will have to begin again)

4.1.2. Options section: you can choose here how the frequencies are going to be used in the

Familias application. “Rest allele” indicates that only the alleles involved in the

calculation are going to exported to Familias (and a “rest allele frequency” will be

also exported so that the sum is 1); and “all alleles” option means that all the alleles

frequencies of each marker will be exported to Familias.

4.1.3. Individuals section: select the number of individuals involved in the calculations

(individuals with known and unknown relationships)

4.1.4. Sheet section: you have to indicate here the sheet in the population Excel file where

your population data was stored and then upload the Excel file. The population Excel

file can be changed during the following steps. A button called “3.Next” will appear

after the upload of the population Excel file. This button allows you to move to the

'Import' tab (it does not work select 'Import' tab directly).

4.2. IMPORT TAB

In this tab you’ll be able to see a button called “4.Load txt Genemapper”. Click on this button

and select the Genemapper file you want to import (created on point 3 in this manual). This file

can be changed during following steps since several samples from the same case could be

analysed in different runs.

See the example:

Once the Genemapper.txt file is uploaded, a new screen showing the content of the file will be

opened. You will also see a cell in the upper part of the screen. Fill in this cell with the name of

the sample you wish (case sensitive) and click the button “Search sample name”. The first

marker of the sample of interest will be automatically located in the GeneMapper file. Write the

position of the first marker of your sample in the cell near button P# (green arrow) and click in

the P# button. The genetic profile will be stored at 'To Familias 1.97 or 3' tab. Repeat the

selection of samples procedure for each individual (you will see as much as P# buttons as the

number of individuals you have selected in the Home tab).

Note that new GeneMapper files can be imported and used for other relatives (P2, P3 and so on)

by using the button 'Load txt Genemapper'.

See the following example where 2 individuals are involved in the kinship: 337 is the position

where the first marker for the first sample of interest is located (individual P1) and 433 is the

one for the second individual (individual P2).

4.3. TO FAMILIAS TAB

Once you have completed the selection of the samples of interest go to the 'To Familias 1.97 or

3' tab directly. You will see a screen showing a table containing all the information loaded from

the previous tab.

You can edit/change any allele from the table (e.g. if OL instead of the desired allele was

imported).

If you want to remove the profiles, press Delete.

Press OK key to save the final txt file in your computer. This is the file you have to open in

Familias 1.97 or 3. Take into account that the selected profiles are now labelled as P1, P2, etc.

You can change these names in Familias (e.g. P1 is the alleged Father, P2 is the son, etc)

THIS IS A BETA VERSION (0.89) OF “GENEMAPPERTOFAMILIAS”. If you have

any comment or suggestions, please contact Antonio Vozmediano

(a.vozme@hotmail.es) or Lourdes Prieto (lourditasmt@gmail.com). All your comments

will be very welcome!